Corrupted output if decontaminating more than one sample using Python API #25
Description
gen_clean_cmd() and gen_paired_clean_cmd() both mutate Aligner.cmd and Aligner.paired_cmd, and since Aligner is instantiated once, templating fails after processing the first fastq / pair of fastqs leading to corruption of the output of subsequent samples when using the Python API. Templating should not mutate Aligner instance. Needs tests for single and paired reads.